TB-Profiler

Lineage	Family	RDs	Frequency
lineage4	Euro-American	None	1.0
lineage4.9	Euro-American (H37Rv-like)	None	0.97

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence	Comment
rrs	1472733	n.888G>A	non_coding_transcript_exon_variant	0.65	streptomycin	Uncertain significance	Mutation from literature

Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence
rrs	1472108	n.263C>T	non_coding_transcript_exon_variant	0.86	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472123	n.278A>T	non_coding_transcript_exon_variant	0.81	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472141	n.296G>A	non_coding_transcript_exon_variant	0.72	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472148	n.303T>C	non_coding_transcript_exon_variant	0.76	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472150	n.305T>A	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472160	n.315C>T	non_coding_transcript_exon_variant	0.82	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472172	n.327T>C	non_coding_transcript_exon_variant	0.15	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472251	n.406G>C	non_coding_transcript_exon_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472258	n.413A>G	non_coding_transcript_exon_variant	0.93	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472259	n.414C>A	non_coding_transcript_exon_variant	0.93	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472530	n.685G>A	non_coding_transcript_exon_variant	0.67	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472537	n.692C>T	non_coding_transcript_exon_variant	0.71	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472544	n.699C>A	non_coding_transcript_exon_variant	0.61	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472545	n.700A>T	non_coding_transcript_exon_variant	0.69	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472566	n.721G>A	non_coding_transcript_exon_variant	0.6	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472571	n.726G>C	non_coding_transcript_exon_variant	0.67	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472580	n.735C>T	non_coding_transcript_exon_variant	0.35	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472581	n.736A>T	non_coding_transcript_exon_variant	0.77	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472584	n.739A>T	non_coding_transcript_exon_variant	0.35	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472598	n.753A>C	non_coding_transcript_exon_variant	0.61	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472599	n.754G>T	non_coding_transcript_exon_variant	0.61	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472616	n.771G>A	non_coding_transcript_exon_variant	0.3	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472655	n.810G>A	non_coding_transcript_exon_variant	0.61	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472658	n.813G>A	non_coding_transcript_exon_variant	0.58	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472661	n.816A>G	non_coding_transcript_exon_variant	0.62	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472713	n.868T>C	non_coding_transcript_exon_variant	0.74	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472714	n.869A>G	non_coding_transcript_exon_variant	0.26	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472716	n.871C>T	non_coding_transcript_exon_variant	0.69	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472742	n.897C>T	non_coding_transcript_exon_variant	0.81	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472744	n.899A>G	non_coding_transcript_exon_variant	0.69	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472755	n.910G>A	non_coding_transcript_exon_variant	0.21	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin
					amikacin	Uncertain significance
rrs	1472781	n.936C>T	non_coding_transcript_exon_variant	0.68	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472790	n.945T>C	non_coding_transcript_exon_variant	0.29	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472793	n.948A>T	non_coding_transcript_exon_variant	0.68	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472803	n.958T>A	non_coding_transcript_exon_variant	0.69	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472824	n.979T>A	non_coding_transcript_exon_variant	0.92	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472828	n.983T>C	non_coding_transcript_exon_variant	0.9	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472895	n.1050C>T	non_coding_transcript_exon_variant	0.85	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472954	n.1109_1111delTCTinsCCC	non_coding_transcript_exon_variant	0.38	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472954	n.1111T>C	non_coding_transcript_exon_variant	0.62	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472957	n.1112C>T	non_coding_transcript_exon_variant	0.45	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472958	n.1113A>G	non_coding_transcript_exon_variant	0.55	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin
					amikacin	Uncertain significance
rrs	1472973	n.1128A>T	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin
					amikacin	Uncertain significance
rrs	1472974	n.1129A>G	non_coding_transcript_exon_variant	0.5	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472988	n.1143T>C	non_coding_transcript_exon_variant	0.62	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin
					amikacin	Uncertain significance
rrs	1472990	n.1145A>G	non_coding_transcript_exon_variant	1.0	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472992	n.1147A>G	non_coding_transcript_exon_variant	0.33	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1473005	n.1160C>T	non_coding_transcript_exon_variant	0.33	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1473035	n.1190G>A	non_coding_transcript_exon_variant	0.96	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473055	n.1210C>T	non_coding_transcript_exon_variant	0.96	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473056	n.1211A>T	non_coding_transcript_exon_variant	0.96	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473066	n.1221A>G	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473088	n.1243A>G	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473100	n.1255G>A	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473104	n.1259C>T	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473110	n.1265T>G	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473111	n.1266A>G	non_coding_transcript_exon_variant	0.94	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473121	n.1276T>C	non_coding_transcript_exon_variant	0.89	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473123	n.1278A>T	non_coding_transcript_exon_variant	0.95	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473148	n.1303G>T	non_coding_transcript_exon_variant	0.61	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1473163	n.1318C>A	non_coding_transcript_exon_variant	0.68	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1473173	n.1328C>T	non_coding_transcript_exon_variant	0.89	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Not assoc w R
					amikacin	Not assoc w R
rrl	1474626	n.969T>C	non_coding_transcript_exon_variant	0.71	capreomycin	Uncertain significance
rrl	1474626	n.969T>C	non_coding_transcript_exon_variant	0.71	linezolid	Uncertain significance
rrl	1474632	n.975G>T	non_coding_transcript_exon_variant	0.65	capreomycin	Uncertain significance
rrl	1474632	n.975G>T	non_coding_transcript_exon_variant	0.65	linezolid	Uncertain significance
rrl	1474634	n.977T>G	non_coding_transcript_exon_variant	0.64	capreomycin
rrl	1474634	n.977T>G	non_coding_transcript_exon_variant	0.64	linezolid
rrl	1474636	n.979_981delACCinsCCG	non_coding_transcript_exon_variant	0.9	capreomycin
rrl	1474636	n.979_981delACCinsCCG	non_coding_transcript_exon_variant	0.9	linezolid
rrl	1474677	n.1020A>G	non_coding_transcript_exon_variant	0.91	capreomycin	Uncertain significance
rrl	1474677	n.1020A>G	non_coding_transcript_exon_variant	0.91	linezolid	Uncertain significance
rrl	1475751	n.2094C>T	non_coding_transcript_exon_variant	0.97	capreomycin
rrl	1475751	n.2094C>T	non_coding_transcript_exon_variant	0.97	linezolid
rrl	1475763	n.2106C>T	non_coding_transcript_exon_variant	0.96	capreomycin	Uncertain significance
rrl	1475763	n.2106C>T	non_coding_transcript_exon_variant	0.96	linezolid
rrl	1475772	n.2115A>C	non_coding_transcript_exon_variant	0.81	capreomycin	Uncertain significance
rrl	1475772	n.2115A>C	non_coding_transcript_exon_variant	0.81	linezolid
rrl	1475774	n.2117C>T	non_coding_transcript_exon_variant	0.16	capreomycin
rrl	1475774	n.2117C>T	non_coding_transcript_exon_variant	0.16	linezolid
rrl	1475777	n.2120A>T	non_coding_transcript_exon_variant	1.0	capreomycin
rrl	1475777	n.2120A>T	non_coding_transcript_exon_variant	1.0	linezolid
rrl	1475881	n.2224T>C	non_coding_transcript_exon_variant	0.96	capreomycin
rrl	1475881	n.2224T>C	non_coding_transcript_exon_variant	0.96	linezolid
rrl	1475883	n.2226A>C	non_coding_transcript_exon_variant	0.99	capreomycin	Uncertain significance
rrl	1475883	n.2226A>C	non_coding_transcript_exon_variant	0.99	linezolid
rrl	1475884	n.2227A>G	non_coding_transcript_exon_variant	0.18	capreomycin	Uncertain significance
rrl	1475884	n.2227A>G	non_coding_transcript_exon_variant	0.18	linezolid	Uncertain significance
rrl	1475892	n.2235A>G	non_coding_transcript_exon_variant	0.77	capreomycin
rrl	1475892	n.2235A>G	non_coding_transcript_exon_variant	0.77	linezolid
rrl	1475897	n.2240T>G	non_coding_transcript_exon_variant	0.78	capreomycin	Uncertain significance
rrl	1475897	n.2240T>G	non_coding_transcript_exon_variant	0.78	linezolid
rrl	1475898	n.2241A>G	non_coding_transcript_exon_variant	0.98	capreomycin	Uncertain significance
rrl	1475898	n.2241A>G	non_coding_transcript_exon_variant	0.98	linezolid
rrl	1475899	n.2242G>A	non_coding_transcript_exon_variant	0.97	capreomycin	Uncertain significance
rrl	1475899	n.2242G>A	non_coding_transcript_exon_variant	0.97	linezolid
rrl	1475900	n.2243A>C	non_coding_transcript_exon_variant	0.93	capreomycin
rrl	1475900	n.2243A>C	non_coding_transcript_exon_variant	0.93	linezolid
rrl	1475906	n.2249C>T	non_coding_transcript_exon_variant	0.81	capreomycin	Uncertain significance
rrl	1475906	n.2249C>T	non_coding_transcript_exon_variant	0.81	linezolid	Uncertain significance
rrl	1475916	n.2259C>G	non_coding_transcript_exon_variant	0.98	capreomycin	Uncertain significance
rrl	1475916	n.2259C>G	non_coding_transcript_exon_variant	0.98	linezolid	Uncertain significance
rrl	1475938	n.2281C>A	non_coding_transcript_exon_variant	0.8	capreomycin
rrl	1475938	n.2281C>A	non_coding_transcript_exon_variant	0.8	linezolid
rrl	1475943	n.2286G>A	non_coding_transcript_exon_variant	0.97	capreomycin	Uncertain significance
rrl	1475943	n.2286G>A	non_coding_transcript_exon_variant	0.97	linezolid	Uncertain significance
rrl	1475945	n.2288C>A	non_coding_transcript_exon_variant	0.97	capreomycin
rrl	1475945	n.2288C>A	non_coding_transcript_exon_variant	0.97	linezolid
rrl	1476332	n.2675G>C	non_coding_transcript_exon_variant	0.9	capreomycin	Uncertain significance
rrl	1476332	n.2675G>C	non_coding_transcript_exon_variant	0.9	linezolid	Uncertain significance
rrl	1476338	n.2681C>T	non_coding_transcript_exon_variant	0.86	capreomycin	Uncertain significance
rrl	1476338	n.2681C>T	non_coding_transcript_exon_variant	0.86	linezolid	Uncertain significance
rrl	1476353	n.2696G>T	non_coding_transcript_exon_variant	0.85	capreomycin	Uncertain significance
rrl	1476353	n.2696G>T	non_coding_transcript_exon_variant	0.85	linezolid	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.87	capreomycin	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.87	linezolid	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.84	capreomycin	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.84	linezolid	Uncertain significance
rrl	1476372	n.2715T>C	non_coding_transcript_exon_variant	0.85	capreomycin	Uncertain significance
rrl	1476372	n.2715T>C	non_coding_transcript_exon_variant	0.85	linezolid	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.83	capreomycin	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.83	linezolid	Uncertain significance
rrl	1476383	n.2726T>A	non_coding_transcript_exon_variant	0.84	capreomycin	Uncertain significance
rrl	1476383	n.2726T>A	non_coding_transcript_exon_variant	0.84	linezolid	Uncertain significance
rrl	1476425	n.2768G>T	non_coding_transcript_exon_variant	0.84	capreomycin	Uncertain significance
rrl	1476425	n.2768G>T	non_coding_transcript_exon_variant	0.84	linezolid	Uncertain significance
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.84	capreomycin	Not assoc w R
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.84	linezolid	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.85	capreomycin	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.85	linezolid	Uncertain significance
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	0.98	capreomycin	Not assoc w R
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	0.98	linezolid	Uncertain significance
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.84	capreomycin	Not assoc w R
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.84	linezolid	Uncertain significance
rrl	1476514	n.2857C>T	non_coding_transcript_exon_variant	0.86	capreomycin	Uncertain significance
rrl	1476514	n.2857C>T	non_coding_transcript_exon_variant	0.86	linezolid	Uncertain significance
rrl	1476519	n.2862C>G	non_coding_transcript_exon_variant	0.85	capreomycin	Uncertain significance
rrl	1476519	n.2862C>G	non_coding_transcript_exon_variant	0.85	linezolid	Uncertain significance
rrl	1476524	n.2867C>A	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1476524	n.2867C>A	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
rrl	1476525	n.2868A>G	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1476525	n.2868A>G	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
rrl	1476530	n.2873C>T	non_coding_transcript_exon_variant	0.85	capreomycin	Uncertain significance
rrl	1476530	n.2873C>T	non_coding_transcript_exon_variant	0.85	linezolid	Uncertain significance

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin	rrs	n.888G>A	Uncertain significance	Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid

TB-Profiler result